Dissertations / Theses on the topic 'Motifs de surface'

In spite of their high abundance and importance, aqueous systems are enigmatic on the microscopic scale. In order to obtain information about their geometrical and electronic structure, simple aqueous solutions have been studied experimentally by photo- and Auger electron spectroscopy using the novel liquid micro-jet technique in conjunction with synchrotron radiation. The thesis is thematically divided into three parts. In the first part we utilize the surface sensitivity of photoelectron spectroscopy to probe the distributions of solutes near the water surface. In agreement with recent theoretical predictions we find that large polarizable anions, such as I- and ClO4-, display enhanced surface propensities compared to smaller rigid ions. Surface effects arising from ion-ion interactions at higher electrolyte concentrations and as function of pH are investigated. Studies of linear mono-carboxylic acids and benzoic acid show that the neutral molecular forms of such weak acids are better stabilized at the water surface than their respective conjugate base forms. The second part examines what type of information core-electron spectra can yield about the chemical state and hydration structure of small organic molecules in water. We demonstrate that the method is sensitive to the protonation state of titratable functional groups and that core-level lineshapes are dependent on local water hydration configurations. Using a combination of photoelectron and X-ray absorption spectroscopy we also show that the electronic re-arrangement upon hydrolysis of aldehydes yields characteristic fingerprints in core-level spectra. In the last part of this thesis we study ultrafast charge delocalization dynamics in aqueous solutions using resonant and off-resonant Auger spectroscopy. Intermolecular Coulombic decay (ICD) is found to occur in a number of core-excited solutions where excess energy is transferred between the solvent and the solute. The rate of ultrafast electron delocalization between hydrogen bonded water molecules upon oxygen 1s resonant core-excitation is found to decrease upon solvation of inorganic ions. The presented work is illustrative of how core-level photoelectron spectroscopy can be valuable in the study of fundamental phenomena in aqueous solutions.

La Réalité Augmentée (RA) vise à afficher des informations numériques virtuelles sur des images réelles. Le recalage est important, puisqu’il permet d'aligner correctement les objets virtuels dans le monde réel. Contrairement au tracking qui recale en utilisant les informations de l’image précédente, la localisation à grande échelle (wide baseline localization) calcule la solution en utilisant uniquement les informations présentes dans l’image courante. Il permet ainsi de trouver des solutions initiales au problème de recalage (initialisation) et, n’est pas sujet aux problèmes de « perte de tracking ». Le problème du recalage en RA est relativement bien étudié dans la littérature, mais les méthodes existantes fonctionnent principalement lorsque la scène augmentée présente des textures. Pourtant, pour le recalage avec les objets peu ou pas texturés, il est possible d’utiliser leurs informations géométriques qui représentent des caractéristiques plus stables que les textures. Cette thèse s’attache au problème de recalage basé sur des informations géométriques, et plus précisément sur les points. Nous proposons deux nouvelles méthodes de recalage de points (RRDM et LGC) robustes et rapides. LGC est une amélioration de la méthode RRDM et peut mettre en correspondance des ensembles de motifs de points 2D ou 3D subissant une transformation dont le type est connu. LGC présente un comportement linéaire en fonction du nombre de points, ce qui permet un tracking en temps-réel. La pertinence de LGC a été illustrée en développant une application de calibration de système projecteur-caméra dont les résultats sont comparables avec l’état de l’art tout en présentant des avantages pour l’utilisateur en termes de taille de mire de calibration
Registration is a very important task in Augmented Reality (AR). It provides the spatial alignment between the real environment and virtual objects. Unlike tracking (which relies on previous frame information), wide baseline localization finds the correct solution from a wide search space, so as to overcome the initialization or tracking failure problems. Nowadays, various wide baseline localization methods have been applied successfully. But for objects with no or little texture, there is still no promising method. One possible solution is to rely on the geometric information, which sometimes does not vary as much as texture or color. This dissertation focuses on new wide baseline localization methods entirely based on geometric information, and more specifically on points. I propose two novel point pattern matching algorithms, RRDM and LGC. Especially, LGC registers 2D or 3D point patterns under any known transformation type and supports multipattern recognitions. It has a linear behavior with respect to the number of points, which allows for real-time tracking. It is applied to multi targets tracking and augmentation, as well as to 3D model registration. A practical method for projector-camera system calibration based on LGC is also proposed. It can be useful for large scale Spatial Augmented Reality (SAR). Besides, I also developed a method to estimate the rotation axis of surface of revolution quickly and precisely on 3D data. It is integrated in a novel framework to reconstruct the surface of revolution on dense SLAM in real-time

Pour une réponse immunitaire efficace, une interaction optimale entre les cellules T et les cellules présentatrices d'antigène (APC) est nécessaire. Elle se présente sous la forme d'un contact cellulaire à différentes échelles allant du moléculaire (1-10 nm) au cellulaire (1-10 micromètres). La liaison entre les récepteurs spéciaux des cellules T (TCR) et leurs ligands sur une APC entraîne une réorganisation moléculaire à plus grande échelle menant d'abord à la formation de micro-clusters de TCR, puis à une restructuration à l'échelle cellulaire de la membrane et du cytosquelette. La création d'un substrat artificiel avec des amas de ligands qui induisent à leur tour l'accumulation de TCR est un outil important pour comprendre le lien entre l'organisation du TCR et de son ligand, l'organisation du cytosquelette d'actine et l'impact de ces deux facteurs sur le comportement cellulaire global, notamment l'adhérence et la signalisation. Nous avons développé un nouveau substrat basé sur la nanotechnologie et utilisé une stratégie alternative basée sur l'auto-assemblage colloïdal pour montrer que le TCR est clairement groupé sur des points de 700 nm et non pas sur des points de 400 nm. L'actine est distribuée de manière homogène sous forme de réseau dans la plupart des cellules, mais dans quelques-unes d'entre elles, elle apparaît sous la forme de points co-localisés avec les amas de ligands. Une observation plus fine à l'aide de la microscopie de reconstruction optique aléatoire indique que les points peuvent en fait être des sites où des faisceaux d'actine se croisent pour former des nœuds non visibles à moindre résolution
For an efficient immune response, an optimal interaction between T-cells and antigen presenting cells (APC) is required; it takes the form of a cell-cell contact involving different scales ranging from the molecular (1-10 nm) to the cellular (1-10 micrometer). The ligation of the special T cell receptors (TCR) to its ligands on an APC, leads to larger scale molecular reorganisation leading first to formation of TCR micro-clusters, and later to cell-scale restructuring of both the membrane and the cytoskeleton. Patterning an artificial substrate with ligand-clusters that in turn induce TCR-clustering is an important tool to understand the link between the organisation of TCR and its ligand, the organisation of the actin cytoskeleton and the impact of both on overall cell behavior including adhesion and signaling. We developed a new nanotechnology based substrate (ligand-dot size down to 250 nm) and also used an alternative strategy based on colloidal self-assembly (700 or 400 nm) to show that TCR is clearly clustered on 700 nm dots but not on smaller 400 nm dots. Actin is homogeneously distributed in the form of a network in most cells but in a few of them, it appears as dots that co-localize with the ligand clusters. Finer observation using stochastic optical reconstruction microscopy indicates that the dots may in fact be sites where actin bundles cross each other forming nodes that are not visible at lower resolution. This work confirms a close link between T cell receptor organisation and actin structure

Otar iosseliani, cineaste georgien, ne en 1934 a tbilissi, est l'auteur d'une oeuvre originale et attachante qui ne compte que peu de films (huit longs-metrages de fiction en plus de trente ans). Mais elle constitue assurement une des plus importantes du cinema contemporain. C'est en tout cas ce que tente de demontrer cette these, en trois temps. D'abord, a travers l'analyse d'un processus de creation tout a la fois philosophique, primitif et teleologique, c'est-a-dire, comparable a celui du demiurge, replace dans la lignee du cinema muet et base sur une methode refusant categoriquement le hasard. Ensuite, en dissequant la fonction du regard du cineaste sur le reel. Que ce soit dans ses documentaires (il en a realise cinq), dans ses trois premiers films tournes en georgie, ou en apprivoisant des cultures etrangeres (principalement la france mais aussi l'afrique), le regard qu'il porte sur le monde fait de lui un cineaste universel. Enfin, en tentant de restituer le plus fidelement possible une des caracteristiques esthetiques de son cinema : le rythme, tant sonore que plastique et structural. Tout au long de ces trois parties, il s'agit egalement de definir l'ethique de iosseliani.

Ce travail de thèse a eu pour objectif de développer de nouvelles méthodes de dépôts et de formation de motifs pour mieux contrôler l'organisation de molécules d'intérêt biologique sur des substrats solides.
Dans la première partie du manuscrit, nous présentons une méthode originale, la micro-aspiration, permettant de réaliser des assemblages réversibles de canaux microfluidiques sur un substrat et servir à guider les liquides. Nous avons étudié les propriétés de ces systèmes avec des modèles physiques simples et appliqué ces phénomènes à la micromanipulation de liquides, le dépôt de protéines à diverses concentrations sur un substrat, la fabrication de motifs de polymères, nanoparticules, gels, etc.
Dans la seconde partie, nous avons exploré des nouvelles méthodes de dépôt de films de phospholipides multicouches sur des substrats solides et les avons appliqués à la fabrication de vésicules unilamellaires géantes de taille contrôlée. Tout d'abord, l'adaptation de techniques conventionnelles (micro-contact printing, moulage, etc.) a permis d'obtenir des motifs de phospholipides de taille micrométrique. Les dépôts ont ensuite été réalisés par retrait d'un ménisque en situation d'évaporation (assemblage capillaire). Nous avons identifié deux régimes de dépôt en fonction de l'importance relative des forces visqueuses et de l'évaporation, permettant un contrôle de l'épaisseur du film jusqu'à 200 nm à la bicouche près. L'émergence d'instabilités de mouillage ou le guidage sur micro-structures ont permis en outre de réaliser des motifs variés. En utilisant des substrats comme électrodes, ces différents niveaux d'organisation ont permis d'obtenir par électroformation des vésicules unilamellaires géantes de taille contrôlée. L'ensemble de ces travaux ouvre de nouvelles voies à la réalisation de surfaces et de motifs micrométriques d'intérêt biologique.

Notre objectif est la modelisation de la formation de complexes proteiques par la recherche de zones de complementarite entre surfaces moleculaires. La complementarite geometrique est une caracteristique indispensable dans la reconnaissance des proteines entre elles, en effet les associations proteiques stables sont dues en particulier aux effets hydrophobiques et aux interactions polaires, qui sont des forces agissant a faible distance. Le probleme de la complementarite moleculaire est aborde par la definition de l'enveloppe convexe d'un nuage tridimensionnel de points. A partir de son enveloppe convexe, on peut definir la profondeur et la hauteur de tout point de la surface moleculaire. La profondeur, definie comme la distance entre le point et la face associee de l'enveloppe convexe, permet de localiser les zones creuses (trous) de la surface moleculaire. La hauteur, definie comme la distance du point a sa face associee sur une surface convexe interne, permet de localiser les zones elevees, (bosses) de la surface moleculaire. Profondeur et hauteur sont ici considerees comme deux quantites complementaires pouvant permettre la recherche de zones complementaires. Chacune des deux surfaces moleculaires est representee par une carte de contour d'iso-profondeur ou d'iso-hauteur, profondeur pour le substrat et hauteur pour l'inhibiteur. Par une comparaison des deux cartes, les zones de complementarite susceptibles de constituer le site de liaison sont selectionnees sur la base de differents criteres de dissemblance: coefficient de correlation, erreur moyenne d'ajustement, indice de non-recouvrement. Cette demarche d'analyse a ete appliquee a l'etude du complexe trypsine-inhibiteur et s'est averee efficace pour retrouver le site de formation du complexe

In silico investigation on protein domains structure and linear/structural motifs can strongly boost functional analyses and technological design. Protein surface features study is crucial to understanding Protein-Protein Interactions (PPI); in particular, surface and pockets conservation and variation, in terms of hydrophobicity, steric hindrance and electrostatics can act as driving forces in protein evolution and functional specialization. Therefore, molecular modeling and structure comparison techniques play an important role in shedding light on “protein behavior” and this PhD work took advantage from integrating computational approaches based on some known molecular modeling methods, such as e.g. Homology Modeling, Fold Recognition, Ab initio Modeling, PBE (Poisson-Boltzmann Electrostatics), Protein-peptide Docking and Hydropathy Analysis with structure and sequence comparison and scanning tools and, of course, with feedback from wet lab analyses performed by co-workers. Such an integrative approach was followed along investigations on a number of different biological systems: • Surface determinants in H5N1 type A Influenza viruses: Here, an analysis of surface determinants from H5N1 haemagglutinin, involved in host-viral interaction, was completed and then published. Genomic variation is very high in influenza A viruses. However, viral evolution and spreading are strongly influenced by immunogenic features and capacity to bind host cells, depending in turn on the two major capsidic proteins (haemagglutinin and neuraminidase). Current analyses of viral evolution are based on serological and primary sequence comparison; however, comparative structural analysis of capsidic proteins can provide functional insights on surface regions possibly crucial to antigenicity and cell binding. We performed molecular modeling and extensive structural comparison of influenza virus haemagglutinin and of their domains and sub-regions to investigate type- and/or domain specific variation. We found that structural closeness and primary sequence similarity are not always tightly related; moreover, type-specific features could be inferred when comparing surface properties of haemagglutinin subregions, monomers and trimers, in terms of electrostatics and hydropathy. Focusing on H5N1, we found that the variation at the receptor binding domain (RBD) surface intriguingly relates to branching of still circulating clades from those ones that are no longer circulating. Recent evidence on the association between electrostatic fingerprints at the haemagglutinin receptor binding surface and the evolutionary success and spreading of H5N1 avian influenza clades prompted us to perform further integrated phylogenetic and structural bioinformatic analysis in H9N2 viruses. In fact, influenza A virus is a zoonotic agent with a significant impact both on public health and poultry industry and switch to human host has been reported for both H5N1 and H9N2 viruses. We performed the evolutionary analysis of a large and non-redundant viral strain dataset, leading to clustering of H9N2 viruses in five groups. Then and according to recent evidence on H5N1, congruence resulted among phylogenetic data and surface electrostatic fingerprints from structural comparison. In particular, surface feature fingerprints could be inferred that relate group specific variation in electrostatic charges and isocontour to well-known hemagglutinin sites involved in modulation of immune escape and host specificity. Results from this second work strengthen suggestion that when integrating up-to-date phylogenetic analyses with sequence-based and structural investigation of surface features may represent a front-end strategy for inferring trends and relevant mechanisms in influenza virus evolution. • Domain architecture variation in mammalian protein trafficking: Human VAMP7b is the most interesting variant among those produced by alternative splicing of the encoding gene SYBL1. Production of VAMP7b variants is determined by skipping of exon 6 which in turn results in coding sequence frameshift. We found that this event is conserved in other mammalian species. VAMP7b shares with the main isoform the N-terminal, inhibitory longin domain and the first half of the SNARE motif. In mammals, VAMP7b is a truncated protein in which the C-terminal half of the SNARE motif and the transmembrane region are replaced by short and variable peptides. Intriguingly instead, only in human and apes sequence frameshift determined by exon 6 skipping results in the creation of a novel unique domain of unknow function, hence human VAMP7b is not truncated but even 40 residues longer than the main isoform. Since existence of such “long” isoform and of its unique domain at protein level were confirmed by specific antibodies, we embarked on in silico dissection of the novel domain by position specific matrix sequence analysis and by ab initio structural modeling. Moreover, since the N-terminal region of the SNARE motif is conserved and it is known to mediate intramolecular binding to the Longin domain, we investigated both in vivo (by two-hybrid in yeast analysis) and in vitro (by NMR analysis) on conservation of the closed conformation. Furthermore, SCL of both VAMP7b and Ykt6b was investigated using GFP and RFP chimeras. Last but not least, b isoforms of the longin genes were analyzed by qPCR and found to be developmentally regulated. • Binding motif regulating neurite outgrowth and guidance: Fine tuning of PPIs by variation in domain architecture or by changing local motifs by surface features modulation can regulate both extracellular and intracellular signaling pathways. Extracellular PPIs can play a central role in heterologous recognition (e.g. host-pathogen) as well as in homologous signaling among cells from the same organism. Proteins exposed at the plasma membrane (PM) can interact each other and with the extracellular matrix (ECM) to provide positional information and guidance cues. Cell adhesion molecules (CAMs) are PM proteins mediating either attractive or repulsive signals by homo- and heterophilic interactions of their extracellular domains (Eds). CAM EDs are most often composed by Ig-like or Fibronectin type III fold repeats. Current evidence suggests that the four N-terminal Ig 1-4 domains of CAM EDs play a major role in such homo- or heterophilic interactions and in particular an important interaction motif is contributed by repeat Ig2. In our lab, biomimetic peptides have been developed by reproducing the known or predicted interaction motifs from the Ig2 domain of human L1CAM and the single Ig domain of human LINGO1, i.e. two proteins that play a crucial role in neurite outgrowth and guidance and in neuronal differentiation. Based on the somehow surprising structural and sequence conservation of the motif region (even when proteins show very different ED architectures), we started investigating on variation and conservation of the putative motif region by means of homology search, regular expression and finally by structural modeling and comparison. Preliminary results highlighted strong conservation of the central Arg residue in the interaction motif, while in other positions of the motif residue properties rather than specific residues are conserved. Such evidence is in agreement with finding that mutation of such residue in L1CAM is responsible for a severe neurological disorder, while mutations at other residues of the motif, results in less severe phenotype. This suggests the motif is an epitope positionally conserved around the central Arg allowing limited, but significant structural variability in surrounding sequence. In order to check such a hypothesis, a structural superposition of the Ig domains containing the interaction motif was performed, confirming that the peptide motif itself is positionally conserved but the highest positional and structural conservation concerns the central Arg residue. Experiments with peptides mutated in the central Arg showed biological activity of these peptides in terms of neuritogenesis signalling. These works carry out a bioinformatic protocol for the characterization of interaction determinants and their functional modulation, easily transportable to other proteins.
Gli studi in silico aventi per oggetto la struttura di domini proteici e di motif sia strutturali che lineari, sono in grado di fornire un importante apporto in termini di comprensione di funzione e nelle biotecnologie. Lo studio delle caratteristiche a carico della superficie proteica si rivelano essenziali nella comprensione delle Interazioni Proteina-Proteina (PPI); in particolare, la conservazione e variazione della superficie proteica e delle relative cavità in termini di idrofobicità, ingombro sterico e caratteristiche elettrostatiche, possono essere considerate come la forza in grado di guidare l’evoluzione e la specializzazione funzionale delle proteine stesse. Alla luce di quanto sopra esposto, tecniche come la Modellistica Molecolare ed il confronto tra strutture giocano un ruolo importante nel chiarire il modus operandi delle proteine e questo progetto di Dottorato ha proprio sfruttato l’approccio integrato di alcune ben note tecniche di biologia computazionale basate sulla Modellistica Molecolare come, ad esempio, Homology Modeling, Fold Recognition, Ab initio Modeling, PBE (Poisson-Boltzmann Electrostatics), Protein-peptide Docking e Hydropathy Analysis con confronto di sequenze e strutture. Elemento indispensabile e prezioso, ovviamente, il feedback ottenuto dagli esperimenti al banco effettuati dai nostri collaboratori. Questo approccio integrato è stato dunque applicato a differenti sistemi biologici: • Individuazione di determinanti di superficie in virus influenzali di tipo A H5N1: è stata effettuata un’analisi dei determinanti di superficie a carico dell’emoagglutinina proveniente dal virus influenzale H5N1, coinvolta nell’interazione virus-ospite. Questo lavoro ha già condotto ad una pubblicazione. La variazione genomica è elevata nei virus influenzali di tipo A. L’evoluzione e la diffusione dei virus sono molto influenzate dalle caratteristiche immunogeniche e dalla capacità del virus, di interagire con le cellule dell’ospite tramite le due più importanti proteine presenti sul capside virale: l’emoagglutinina e la neuraminidasi. Le analisi oggi a disposizione sono basate sul confronto dell’attività sierologica e di sequenze primarie; alla luce di ciò, l’analisi strutturale di queste proteine capsidiche può essere in grado di svelare delle conoscenze a riguardo di certe regioni presenti sulla superficie proteica che possono essere cruciali per l’antigenicità e per il legame alle cellule dell’ospite. L’emoagglutinina, sezionata nei suoi domini e subdomini, è stata da noi studiata con metodi di Modellistica Molecolare e sottoposta a confronti strutturali fini, per individuare quelle variazioni che potessero risultare tipo/dominio specifiche. Abbiamo evidenziato che la vicinanza strutturale e la similarità di sequenza primaria non sempre sono correlate; in più, caratteristiche tipo-specifiche di sottoregioni dell’emoagglutinina, monomeri e trimeri, possono essere rivelate grazie al confronto delle loro proprietà di superficie, (in termini di elettrostatica ed idrofobicità) appartenenti a sottoregioni dell’emoagglutinina, monomeri e trimeri. In questo lavoro ci siamo focalizzati sul virus H5N1 e abbiamo scoperto che il dominio di legame recettoriale dell’emoagglutinina (RBD) presenta delle variazioni tra clade circolanti e non più circolanti. Le recenti scoperte riguardanti l’associazione tra la disposizione delle cariche al RBD ed il successo in termini evolutivi e di diffusione del virus H5N1 ci hanno spinto ad eseguire analisi integrate di filogenesi e biologia strutturale a carico dei virus H9N2. Infatti, l’influenza A è un agente zoonotico in grado di produrre un grosso impatto sia sulla salute pubblica che sull’industria del pollame, avendo la capacità di effettuare il salto d’ospite, come riportato proprio per H5N1 ed H9N2. Abbiamo effettuato un’analisi evoluzionistica su un grande dataset non ridondante di ceppi virali e questo ci ha consentito di individuare cinque gruppi di virus H9N2. In accordo con le precedenti analisi effettuate per H5N1, abbiamo ottenuto accordo tra i dati filogenetici con quelli ottenuti dalle analisi di confronto strutturale. In particolare, emerge che la variazione della disposizione delle cariche coincide con quella di siti noti dell’emoagglutinina coinvolti nell’evasione al sistema immunitario e nella specificità d’ospite. I risultati ottenuti da questo secondo lavoro pongono l’accento sull’importanza dell’integrazione tra analisi di tipo filogenetiche e di biologia strutturale nella scoperta di nuovi meccanismi evolutivi dei virus dell’influenza. • Variazione dell’architettura di domini in proteine di mammifero coinvolte nel traffico vescicolare: la proteina umana VAMP7b è la più interessante tra quelle prodotte per splicing alternativo del gene SYBL1. La produzione di VAMP7b è causata dal salto dell’esone 6 che si traduce in uno slittamento della sequenza codificante. Abbiamo scoperto che questo evento è conservato in altre specie di mammiferi. VAMP7b condivide con l’isoforma principale il dominio inibitorio longin N-terminale e la prima metà dello SNARE motif. Nei mammiferi, VAMP7b è una proteina tronca in cui al C-terminale metà dello SNARE motif e la regione transmembrana sono sostituite da peptidi corti e variabili. È molto interessante notare come negli uomini e nelle scimmie antropomorfe lo slittamento della regione codificante determinato dal salto dell’esone 6 abbia prodotto un nuovo dominio di funzione sconosciuta: proprio per questo VAMP7b umana non è tronca, ma addirittura 40 residui più lunga rispetto all’isoforma principale. Dal momento che l’esistenza di questa isoforma “lunga” ed il suo nuovo dominio sono stati confermati a livello proteico grazie all’ausilio di specifici anticorpi, abbiamo effettuato una dissezione in silico del nuovo dominio adoperando un’analisi di sequenza di tipo matrice posizione-specifica (PSI-BLAST), seguita da da Modellistica Strutturale di tipo ab initio. In più, dal momento che la regione N-terminale dello SNARE motif è conservata ed è nota nel mediare il legame intramolecolare al dominio Longin, abbiamo appurato la conservazione della conformazione chiusa sia in vivo (saggio del doppio ibrido in lievito) che in vitro (analisi NMR). Inoltre, la localizzazione subcellulare (SCL) di VAMP7b e Ykt6b è stata studiata adoperando chimere contenenti GFP e RFP. Non ultimo, le isoforme b dei geni longin sono stati analizzati tramite qPCR e si è scoperto essere regolate durante lo sviluppo. • Motif di legame con azione regolatoria sulla crescita e l’indirizzamento neuronale: La regolazione fine delle interazioni proteina-proteina che avviene grazie alle variazioni nell’architettura dei domini o dal cambiamento di motif locali indotto dalla modulazione di caratteristiche di superficie, è in grado di regolare i percorsi di segnalazione sia a livello intra- che extracellulare. Le interazioni proteina-proteina extracellulari possono giocare un ruolo fondamentale nel riconoscimento eterologo (es. ospite-patogeno) come nella segnalazione omologa tra cellule appartenenti allo stesso organismo. Le proteine esposte in membrana plasmatica (PM) possono interagire le une con le altre e con la matrice extracellulare (ECM) per consentire informazioni posizionali e segnali di indirizzamento. Le molecole di adesione cellulare (CAMs) sono proteine della membrana plasmatica in grado di mediare segnali sia di natura attrattiva che repulsiva grazie ad interazioni omo- ed eterofiliche a carico dei loro domini extracellulari (EDs). Questi ultimi sono composti per la magior parte da domini ripetuti aventi fold di tipo Ig o Fibronectina di tipo III. Le attuali conoscenze suggeriscono che i 4 domini extracellulari N-terminali di tipo Ig siano importanti nelle interazioni omo- o eterofiliche ed in modo particolare il dominio Ig2 è provvisto di un importante motif di interazione. Nel nostro laboratorio abbiamo sviluppato dei peptidi biomimetici che riproducono i motif di interazione conosciuti o predetti appartenenti al dominio Ig2 di L1CAM umana e al singolo dominio Ig di LINGO1 umana, proteine, queste, che giocano un ruolo fondamentale nella crescita, nell’indirizzamento e nel differenziamento neuronale. Sulla base della conservazione strutturale della regione del motif (anche tra proteine con architetture molto diverse dei loro EDs), abbiamo iniziato a studiarne la variazione di sequenza mediante analisi per omologia e per espressioni regolari, per infine tornare al livello strutturale mediante Modellistica Molecolare. I risultati preliminari indicano una forte conservazione dell’Arginina centrale presente nel motif d’interazione, mentre nelle altre posizioni del motif si osserva la conservazione di proprietà dei residui piuttosto che la presenza di specifici residui. Questa evidenza è in accordo con il dato di fatto che la mutazione dell’Arginina in L1CAM è responsabile di un serio disordine neurologico, mentre mutazioni a carico di altri residui del motif causano un fenotipo meno grave. Questo suggerisce che il motif è un epitopo posizionalmente conservato attorno all’Arginina centrale in grado di consentire una variabilità limitata ma significativa nella sequenza circostante. Per verificare quest’ipotesi è stata effettuata una superimposizione strutturale dei domini Ig contenenti il motif d’interazione: il risultato ha confermato che il peptide contenente il motif è di per sé conservato posizionalmente e che la conservazione maggiore sia a livello posizionale che struturale è a carico del residuo centrale di Arginina. Esperimenti con peptidi mutati nell’Arginina centrale hanno dimostrato un’attività in termini di segnalazione nella neuritogenesi. Questi lavori hanno consentito di sviluppare un protocollo bioinformatico per la caratterizzazione di determinanti d’interazione e della loro modulazione funzionale, facilmente trasportabile su altre proteine.

Dans ce manuscrit, nous étudions la réponse mécanique de films minces d'hydrogel sous plusieurs angles, incluant celui d’instabilités de la surface libre, d’indentation de la surface au moyen d’un fluide et de situations proches du contact de Hertz. Un premier chapitre préliminaire est consacré à la présentation des concepts de base utilisés dans cette thèse. Ensuite, dans une première partie, nous nous intéressons à des instabilités de surface induites par gonflement, que l'on observe à la fois sur des hydrogels gonflés et sur des films séchés. Nous analysons la formation de motifs comme le résultat d'un important gonflement anisotrope des films qui sont attachés à une surface, suivi du séchage de la surface libre de l'hydrogel de polymères, d'ores et déjà déstabilisée. Dans une deuxième partie, nous développons un modèle poroélastique pour décrire la réponse mécanique d'un hydrogel perméable soumis à un quelconque champ de pression possédant une symétrie axiale, dans un cas général. Aussi bien le cas d'une épaisseur infinie que les effets de taille finie sont étudiés et comparés. Dans une troisième partie, nous utilisons ce cadre théorique pour aborder le problème spécifique du couplage entre poroélasticité et lubrification, rencontré dans le cadre de techniques en sonde colloïdale et sans contact. Nous aboutissons théoriquement aux composantes dissipative et conservative de la force résultant du mouvement vertical d'une sphère au voisinage du substrat poroélastique. Ces résultats théoriques sont confrontés à des résultats expérimentaux de Microscopie à Force Atomique (AFM) en sonde colloïdale, obtenus sur un hydrogel épais et gonflé. Dans une dernière partie, nous mettons en évidence une succession de réponses mécaniques de la part d'hydrogels gonflés, avec des expériences d'Appareil à Forces de Surface (SFA). Partant d'un régime dénué d'interactions entre la sonde et le gel, la surface de l'hydrogel subit d'abord une faible déformation, dans un régime en lubrification. Enfin, nous montrons qu'à température ambiante la contrainte mécanique imposée déclenche par déshydratation la transition vitreuse du polymère. Dans l’ensemble, les résultats obtenus montrent que la réponse poroélastique est caractérisée par une transition dans le temps allant d’un comportement purement élastique et incompressible à un comportement purement élastique et compressible
In this manuscript, we study the mechanical response of hydrogel thin films from different perspectives, including free-surface instability, fluid-mediated surface indentation and Hertz-like contact situations. A first, preliminary Chapter is deduced to the introduction of basic concepts used is this thesis. Then, in a first part, we focus on swelling-induced surface instabilities that are observed on both swollen hydrogels and dried polymer films. The different observed morphologies are characterized by shape and spacing. We analyse the pattern formation as the result of an important anisotropic swelling of surface-attached films, and a subsequent drying of the already-destabilized free surface of polymer hydrogel. In a second part, we develop a poroelastic model to describe the mechanical response of a permeable hydrogel to any axially-symmetric pressure field, in a general case. Both the infinite-thickness case and finite-size effects are studied and compared. In a third part, we use the latter theoretical framework to address the specific poroelastic lubrication coupling associated with contactless colloidal-probe methods. We derive theoretically the conservative and dissipative components of the force associated with the oscillating vertical motion of a sphere close to the poroelastic substrate. We confront our theoretical results to colloidal-probe Atomic Force Microscopy (AFM) experiments performed on a thick and swollen hydrogel. In a last part, we highlight a succession of several mechanical responses of swollen hydrogels, with Surface Force Apparatus (SFA) experiments. From a regime with no gel-probe interaction, the hydrogel first undergoes a gentle deformation of its surface in a lubricated regime. Then, the indentation of the probe in a contact regime forces the expulsion of the solvent from the polymer matrix. We finally show that, at room temperature, the imposed mechanical load triggers the dehydration-induced glass transition of the polymer. Overall, our results show that the poroelastic response is characterized by a transition in time from a purely elastic and incompressible behaviour to a purely elastic and compressible one

Des motifs nanométriques d’oxydes métalliques (TiO2, Al2O3, ZrO2) étaient synthétisés avec une technique bottom-up. Un mélange de précurseurs moléculaires et de micelles préformées des copolymères à block est déposé sur des substrats tels que la silice, l’or ou l’ITO par voie de trempage. Des monocouches de micelles entourées par les espèces inorganiques sont deposées à des concentrations et des vitesses de dépôt faibles. Calcination élimine les copolymères et des motifs (perforations rondes, canaux, anneaux,…) rigides d’oxyde métallique sont obtenus. La présence de monocouches de perforations d’un diamètre entre 10 et 70nm ainsi que l’accessibilité de la surface du substrat a travers ces perforations a été confirme avec plusieurs méthodes de caractérisation. Les dessins du type nanocrateres sont bifunctionels, peuvent être functionalisé sélectivement et ont une bonne stabilité mécanique, thermique et chimique ce qui fait que ces matériaux sont intéressants pour plusieurs applications
Metal oxide nanopatterns (TiO2, Al2O3, ZrO2) were synthesised with a bottom up technique that combines the method of chemical solution deposition and the self-organisation properties of block copolymer micelles on a substrate surface through Evaporation Induced Micelle Packing (EIMP). Molecular precursors were mixed with micelles in EtOH/THF/H2O or EtOH/THF and the solutions were dip coated onto various substrates such as silicon wafers, gold or ITO. High dilution and low withdrawal speed lead to the deposition of micelle monolayers surrounded by inorganic precursors. A calcination step eliminates the block copolymer and rigid metal oxide nanopatterns with various motifs like circular perforations (nanocraters), channels or rings are obtained. The size and kind of the motifs can be controlled by adjusting several crucial parameters during solution preparation like the kind and size of the used block copolymer in combination with the used solvent composition, concentration and conditioning. High kinetics of evaporation during the dip coating further allow ordering of nanocrater perforations in hexagonal patterns. The synthesised patterns were characterised by ellipsometry, AFM, FEG-SEM, GISAXS, XPS, cyclic voltametry and contact angle measurements. The presence of monolayers of perforations with diameters of 10-70nm and accessibility of the substrate surface through the perforations was confirmed. Nanocrater patterns show inherent bifunctionality and the substrate surface and the pattern can be selectively functionalised. In addition, nanocrater patterns are mechanically, chemically and thermally stable and are therefore interesting materials for various kinds of applications

A sequential series of mutational events is necessary for the development of leukemia. The misexpression of TAL1, a basic helix-loop-helix (bHLH) transcription factor, is the most common mutation in T cell acute lymphoblastic leukemia (T-ALL). Tal1 transgenic mice develop leukemia with a long latency and incomplete penetrance indicating additional mutations are necessary to develop disease. To investigate additional mutational events that potentially contribute to TAL1-expressing T-ALL patients, we sought to identify cooperating mutations in Tal1 transgenic mice. Clinical studies implicated the loss of the INK4a/ARF locus, which encodes two tumor suppressors, p16INK4a and p14ARF, in the majority of T-ALL patients. We demonstrated disease acceleration in tal1/ink4a/arf+/-, tal1/pl6ink4a+/- and tal1/p19arf+/- mice, thereby providing genetic evidence that Tal1 cooperates with loss of either p16Ink4a or p19Arf in leukemogenesis. The cooperation of Tal1 with the loss of or p16Ink4a or p19Arf, is consistent with our observation that Tal1 alters cell cycle regulation in leukemia by promoting S phase induction and apoptosis in vivo. An additional mutational event common in tal1 tumors is activation of the Notch1 signaling pathway. We provide evidence that the majority of tal1 tumors express increased levels of Notch1, and exhibit activating notch1 mutations. Additionally, tal1 tumors display sensitivity to the pharmacologic inhibition of γ-secretase activity in vitro, indicating that γ-secretase inhibitors may prove an efficacious treatment for TAL1-expressing T-ALL patients. Furthermore, we developed a doxycycline-regulated NotchIC T-ALL cell line, which will allow the identification of important Notch1IC target genes in leukemogenesis.

Cette thèse traite du suivi temporel de surfaces déformables. Ces surfaces sont observées depuis plusieurs points de vue par des caméras qui capturent l'évolution de la scène et l'enregistrent sous la forme de vidéos. Du fait des progrès récents en reconstruction multi-vue, cet ensemble de vidéos peut être converti en une série de clichés tridimensionnels qui capturent l'apparence et la forme des objets dans la scène. Le problème au coeur des travaux rapportés par cette thèse est de complémenter les informations d'apparence et de forme avec des informations sur les mouvements et les déformations des objets. En d'autres mots, il s'agit de mesurer la trajectoire de chacun des points sur les surfaces observées. Ceci est un problème difficile car les vidéos capturées ne sont que des séquences d'images, et car les formes reconstruites à chaque instant le sont indépendemment les unes des autres. Si le cerveau humain excelle à recréer l'illusion de mouvement à partir de ces clichés, leur utilisation pour la mesure automatisée du mouvement reste une question largement ouverte. La majorité des précédents travaux sur le sujet se sont focalisés sur la capture du mouvement humain et ont bénéficié de la nature articulée de ce mouvement qui pouvait être utilisé comme a-priori dans les calculs. La spécificité des développements présentés ici réside dans la généricité des méthodes qui permettent de capturer des scènes dynamiques plus complexes contenant plusieurs acteurs et différents objets déformables de nature inconnue a priori. Pour suivre les surfaces de la façon la plus générique possible, nous formulons le problème comme celui de l'alignement géométrique de surfaces, et déformons un maillage de référence pour l'aligner avec les maillages indépendemment reconstruits de la séquence. Nous présentons un ensemble d'algorithmes et d'outils numériques intégrés dans une chaîne de traitements dont le résultat est un maillage animé. Notre première contribution est une méthode de déformation de maillage qui divise la surface en une collection de morceaux élémentaires de surfaces que nous nommons patches. Ces patches sont organisés dans un graphe de déformation, et une force est appliquée sur cette structure pour émuler une déformation élastique par rapport à la pose de référence. Comme seconde contribution, nous présentons une formulation probabiliste de l'alignement de surfaces déformables qui modélise explicitement le bruit dans le processus d'acquisition. Pour finir, nous étudions dans quelle mesure les a-prioris sur la nature articulée du mouvement peuvent aider, et comparons différents modèles de déformation à une méthode de suivi de squelette. Les développements rapportés par cette thèse sont validés par de nombreuses expériences sur une variété de séquences. Ces résultats montrent qu'en dépit d'a-prioris moins forts sur les surfaces suivies, les idées présentées permettent de traiter des scènes complexes contenant de multiples objets tout en se comportant de façon robuste vis-a-vis de données fragmentaires et d'erreurs de reconstruction
In this thesis we address the problem of digitizing the motion of three-dimensional shapes that move and deform in time. These shapes are observed from several points of view with cameras that record the scene's evolution as videos. Using available reconstruction methods, these videos can be converted into a sequence of three-dimensional snapshots that capture the appearance and shape of the objects in the scene. The focus of this thesis is to complement appearance and shape with information on the motion and deformation of objects. In other words, we want to measure the trajectory of every point on the observed surfaces. This is a challenging problem because the captured videos are only sequences of images, and the reconstructed shapes are built independently from each other. While the human brain excels at recreating the illusion of motion from these snapshots, using them to automatically measure motion is still largely an open problem. The majority of prior works on the subject has focused on tracking the performance of one human actor, and used the strong prior knowledge on the articulated nature of human motion to handle the ambiguity and noise inherent to visual data. In contrast, the presented developments consist of generic methods that allow to digitize scenes involving several humans and deformable objects of arbitrary nature. To perform surface tracking as generically as possible, we formulate the problem as the geometric registration of surfaces and deform a reference mesh to fit a sequence of independently reconstructed meshes. We introduce a set of algorithms and numerical tools that integrate into a pipeline whose output is an animated mesh. Our first contribution consists of a generic mesh deformation model and numerical optimization framework that divides the tracked surface into a collection of patches, organizes these patches in a deformation graph and emulates elastic behavior with respect to the reference pose. As a second contribution, we present a probabilistic formulation of deformable surface registration that embeds the inference in an Expectation-Maximization framework that explicitly accounts for the noise and in the acquisition. As a third contribution, we look at how prior knowledge can be used when tracking articulated objects, and compare different deformation model with skeletal-based tracking. The studies reported by this thesis are supported by extensive experiments on various 4D datasets. They show that in spite of weaker assumption on the nature of the tracked objects, the presented ideas allow to process complex scenes involving several arbitrary objects, while robustly handling missing data and relatively large reconstruction artifacts

L'objectif de cette thèse est le développement d'une langue électronique avec une méthode simplifiée d'obtention de récepteurs à réactivité croisée. Ces récepteurs sont préparés par une approche combinatoire novatrice qui consiste au mélange et à l'auto-assemblage de deux disaccharides. Le couplage de ces récepteurs avec un système de détection d'imagerie par résonance des plasmons de surface nous a permis de réaliser une langue électronique capable de différencier des échantillons de différentes complexités, y compris des protéines pures et des mélanges complexes. Cela se fait grâce aux profils et images d'évolution continue, assimilés à des « empreintes digitales » des échantillons. D'un autre côté, ce système peut être utilisé en tant qu'outil pour la conception de surfaces biomimétiques 2D et 3D. Ce système est prometteur pour l'étude des interactions sucre-protéine et pour la préparation de nanovecteurs biomimétiques qui ciblent de façon spécifique des protéines d'intérêt
L'objectif de cette thèse est le développement d'une langue électronique avec une méthode simplifiée d'obtention de récepteurs à réactivité croisée. Ces récepteurs sont préparés par une approche combinatoire novatrice qui consiste au mélange et à l'auto-assemblage de deux disaccharides. Le couplage de ces récepteurs avec un système de détection d'imagerie par résonance des plasmons de surface nous a permis de réaliser une langue électronique capable de différencier des échantillons de différentes complexités, y compris des protéines pures et des mélanges complexes. Cela se fait grâce aux profils et images d'évolution continue, assimilés à des « empreintes digitales » des échantillons. D'un autre côté, ce système peut être utilisé en tant qu'outil pour la conception de surfaces biomimétiques 2D et 3D. Ce système est prometteur pour l'étude des interactions sucre-protéine et pour la préparation de nanovecteurs biomimétiques qui ciblent de façon spécifique des protéines d'intérêt

The presented dissertation is concerned with anisotropic curvature motion of two-dimensional parametric surfaces as well as their application in surface fairing and surface restauration. Mainly the so called anisotropic mean curvature motion (AMCM) and the anisotropic Willmore-flow are being treated. These flows are generalizations of the classical mean curvature flow and the classical Willmore-flow, respectively. The anisotropies are induced by positive, 1-homogenous and convex functions, which can be regarded as support functions of convex bodies, so called Wulff-shapes. Being a method of fourth order of differentiation in the surface coordinates, the anisotropic Willmore-flow allows the prescription of boundary values for the position of the boundary itself as well as for the surface normals on the boundary of a surface patch under consideration. Hence it is an appropriate method for the reconstruction of partially destroyed surfaces. In this work a numerical scheme for the anisotropic Willmore-flow is presented, which is based on an operator splitting of the fourth order evolution equation into two weak equations of first order of differentiation, which is discretized using linear finite elements in space. In particular the discretization of the AMCM turns out to be one of these equations. Based on the AMCM a method for the fairing of surfaces with crystalline edges is developed. Modifications of the discrete AMCM are also used for surface modeling purposes. Schemes for the artificial aging and for virtual engraving of surfaces are presented. Further on a subdivision scheme based on the isotropic mean curvature motion is introduced. Finally, the isotropic as well as the anisotropic Willmore-flow is employed for the restauration of partially destroyed triangulated surfaces.

Traditional studies on the image motion of specularities have concentrated on the motion of isolated specular patches on known specular surfaces, where important parameters such as surface curvature are predetermined. Furthermore the considered surfaces are mostly convex and non-undulating. Here, I attempt to expand on some of the previous results, by examining the frequency characteristics of the global motion of specular markings on random, undulating surfaces subject to a lateral camera motion with constant velocity. I first expand the notion of a bowtie in the Fourier domain introduced by Langer and Mann[7] to accommodate the case of a smooth undulating surface, and then attempt to show that in most cases the global motion of the specular components for the considered surface and motion display roughly a similar power spectrum signature as the Lambertian components, characterized by a continuum of motions plane intersecting at the origin, which I call a blurred bowtie. The subtle discrepancies between the frequency profile of the Lambertian and specular components are also examined in the scope of this thesis.

The ultimate goal of this project has been to develop a computational model for quantifying the interactions between of a body of fluid and a fibrous surface. To achieve this goal, one has to develop a model to create virtual structures that resemble the morphology of a fibrous surface (Objective-1) as well as a model that can simulate the flow of a fluid over these virtual surfaces (Objective-2). To achieve the first objective, we treated fibers as an array of beads interconnected through viscoelastic elements (springs and dampers). The uniqueness of our algorithm lies in its ability to simulate the curvature of the fibers in terms of their rigidity, fiber diameter, and fiber orientation. Moving on to Objective-2, we considered woven screens for their geometric periodicity, as a starting point. We studied how fiber diameter, fiber spacing, and contact angle can affect the skin-friction drag of a submerged hydrophobic woven screen, and how such surfaces resist against water intrusion under elevated hydro-static pressures (a requirement for providing drag reduction benefits). We also studied the impact of surface geometry and wetting properties on droplet mobility over these surfaces. Laboratory experiment was conducted at various stages throughout this investigation, and good agreement was observed between the experimental data and the results from our numerical simulation.

Un liquide ruisselant d?un surplomb solide peut présenter une dynamique complexe, associée à des effets conjugués de surface libre et de gravité. Notre cadre d?étude utilise des liquides appropriés (mouillants et visqueux) sous alimentation continue. Pour de faibles débits, le liquide ruisselle en gouttes, alors qu?à débit supérieur, il se forme un motif de colonnes liquides. Ce motif décrit un cercle, si le surplomb est une coupelle circulaire. Dans cette " fontaine ", les colonnes ont des mouvements collectifs : dérive par paquets, oscillations, chaos spatio-temporel. Le chaos se traduit par l?apparition de défauts dans la structure spatio-temporelle du motif (nombre de colonnes non-constant), qui engendrent l?imprédictibilité. A débit élevé, le liquide adopte la forme d?une nappe tombante. Le cas du rideau liquide formé à partir d?un cylindre débordant a permis l?étude de sillages et de trous dans la nappe, ainsi que d?une instabilité propagative se structurant en damier.

Turbulence research in the laboratory has confirmed the existence of quasi-coherent structures amidst the chaos of a turbulent boundary layer. It has been observed that a quasi-periodic phenomena called “bursting” accounts for a major contribution to the turbulent Reynolds stress and the production of turbulent kinetic energy. Bursting is the term used for a sequence of events, where a low-speed streak of fluid from the near wall region lifts away from the wall, slowly at first, and then rapidly moves away from the wall as it convects downstream where it becomes unstable and breaks up violently upon interaction with the outer flow. This ejection of low speed fluid into the mean flow is responsible for locally high values of turbulent kinetic energy. Although a great deal is known about these structures in laboratory flows, little has been done to investigate if such structures are universal in turbulent flows, i.e., their existence in large Reynolds number flows such as the turbulent air flow over the ocean. It would seem, intuitively, that such structures, if present in the marine atmospheric boundary layer, would play a major role in the transfer of momentum, mass and heat across the air-sea interface. It is speculated that these motions may also be associated with large scale organized motions in wall bounded turbulent shear flows. The effort aimed at elucidating the physics underlying such structures would be invaluable in contributing to our understanding of the air-sea flux mechanism. In this dissertation, standard ejection detection schemes like the quadrant, the VITA and the modified u-level techniques have been applied to turbulent wind data measured over the ocean to confirm the existence of burst like structures. The proportions of contributions to the Reynolds stress from the four quadrants of the u’w’ plane are in close agreement with the corresponding contributions for a laboratory flow. Ejection detection followed by the grouping of ejections into bursts yielded a mean burst period of 47 s, at a height of 8.2 m above the water surface, where the mean wind velocity was 6.74 m/s. This burst period corresponds well with the peaks obtained from the autocorrelation of the streamwise velocity signal and the first moment of the stress spectrum, confirming the quasi-periodic nature of this phenomena. Furthermore, phase averages of these events show a structure which is similar to the structure of events detected in laboratory flows. The ejection periods are seen to decrease with increasing wind speed. The burst periods decrease at first with increasing wind speed and then appear to attain a constant value after a wind speed of 6-7 m/s. This has been attributed to the breakdown of the grouping algorithm at higher wind speeds. Ejection and burst frequencies exhibit no discernible dependence on the surface wave field. Ejection and sweep motions have been studied at various length scales. The original velocity signal is bandpass filtered for various frequency bands. For each band, the percentage contributions to the Reynolds stress from the quadrants of the u'w’ plane are close to the corresponding quadrant contributions of the other bands. This indicates similar turbulence structure at different scales. The velocity signals for each band have been normalized by their root mean square (RMS) value. Visualizing the signals on nondimensional time shows the signals from each band to be very similar. These results can also be interpreted as evidence for the ejection and sweep motions existing simultaneously at different scales, indicating the fractal nature of these events. Large scale motions, which appear to be associated with ejection and sweep motions, have been identified in the marine atmospheric surface layer using velocity probe measurements at multiple heights. Visualizing these velocity signals suggests that the organized features extend across the depth of the surface layer. Converting the temporal signals to spatial fluctuations suggests that these structures are inclined at an angle while convecting downstream. The inclination angle near the surface (z < 18 m) is approximately 15° and it increases with increasing height to about 45° when z = 45 m. The spatial velocity fluctuations also indicate that these organized features may be large transverse vortical arches.
Ph. D.

Tracking human hand motions has raised more attention due to the recent advancements of virtual reality (Rheingold, 1991) and prosthesis control (Antfolk et al., 2010). Surface electromyography (sEMG) has been the predominant method for sensing electrical activity in biomechanical studies, and has also been applied to motion tracking in recent years. While most studies focus on the classification of human hand motions within a predefined motion set, the prediction of continuous finger joint angles and wrist angles remains a challenging endeavor. In this research, a biomechanical knowledge-driven data fusion strategy is proposed to predict finger joint angles and wrist angles. This strategy combines time series data of sEMG signals and simulated muscle features, which can be extracted from a biomechanical model available in OpenSim (Delp et al., 2007). A support vector regression (SVR) model is used to firstly predict muscle features from sEMG signals and then to predict joint angles from the estimated muscle features. A set of motion data containing 10 types of motions from 12 participants was collected from an institutional review board approved experiment. A hypothesis was tested to validate whether adding the simulated muscle features would significantly improve the prediction performance. The study indicates that the biomechanical knowledge-driven data fusion strategy will improve the prediction of new types of human hand motions. The results indicate that the proposed strategy significantly outperforms the benchmark date-driven model especially when the users were performing unknown types of motions from the model training stage. The proposed model provides a possible approach to integrate the simulation models and data fusion models in human factors and ergonomics.
Master of Science

A theoretical design by Balazs et al (ACS Nano, 2008), in which two particles are propelled forward by changing their interaction with a compliant surface by releasing nanoparticles, was attempted to be implemented. Initial studies showed that the design needed to be altered slightly to overcome the friction encountered between the particles and the surface, and to alter the surface by a way other than by the adsorption of nanoparticles. These alterations to the design included changing the interactions present from totally adhesive, to partially or completely repulsive to overcome friction, and substituted a catalytic chemical reaction for the release of nanoparticles used in theoretical design. An implementation of the theoretical design which used repulsive van der Waals forces to change the particle-surface interaction from adhesive to repulsive, by the catalytic conversion of benzene and bromine to bromobenzene, was investigated. It was found that although the particle-surface interaction could be converted from attractive to repulsive, the rate of the catalytic reaction was too slow to surround the catalytic particles with enough bromobenzene to propel particles forward. Electrostatic repulsions between a particle and surface were investigated and found to be unable to significantly change the particle-surface interaction, so were of no use in implementing the theoretical design. Another implementation of the theoretical design which used the steric forces exerted between a particle and surface to alter the particle-surface interaction was investigated. It was found that these steric interactions could significantly influence particles and were able to control their position on a surface. Ways to change the steric interactions from repulsive to more repulsive by a chemical reaction were found and catalytic particles which could release the required reagent created. In all cases it was found that the rate of catalytic reaction was too slow to modify the surface in the correct way to produce propulsion. It was concluded that substituting a catalytic chemical reaction for the release of nanoparticles in the theoretical design is not a viable alternative which can be used to alter a surface and thus change the particle-surface interaction to create propulsion.

We propose a new dynamically feasible trajectory generation algorithm that incorporates sternward motion for unmanned surface vehicles. This work is motivated by riverine applications where the operating environment is large and poorly known. We extend a navigation approach for forward path planning into a more versatile framework that includes safe and dynamically feasible backward trajectories. We pose the backward trajectory generation problem as a finite-horizon optimal control problem and transform it into a nonlinear programming problem by utilizing the direct shooting method. The nonlinear programming problem is solved using the Hooke-Jeeves numerical algorithm. We provide successful simulation and field-trial results that demonstrate the performance of backward path planning algorithm.
Master of Science

At the microscopic level, many materials are made of smaller and randomly oriented grains. These grains are separated by grain boundaries which tend to decrease the electrical and thermal conductivity of the material. The motion of grain boundaries is an important phenomenon controlling the grain growth in materials processing and synthesis. Mathematical modeling and simulation is a powerful tool for studying the motion of grain boundaries. The research reported in this thesis is focused on the numerical simulation and analysis of a coupled surface and grain boundary motion which models the evolution of grain boundary and the diffusion of the free surface during the process of grain growth. The “quarter loop” geometry provides a convenient model for the study of this coupled motion. Two types of normal curve velocities are involved in this model: motion by mean curvature and motion by surface diffusion. They are coupled together at a triple junction. A front tracking method is used to simulate the migration. To describe the problem, different formulations are presented and discussed. A new formulation that comprises partial differential equations and algebraic equations is proposed. It preserves arc length parametrization up to scaling and exhibits good numerical performance. This formulation is shown to be well-posed in a reduced, linear setting. Numerical simulations are implemented and compared for all formulations. The new formulation is also applied to some other related problems. We investigate numerically the linear stability of the travelling wave solutions for the quarter loop problem and a simple grain boundary motion problem for both curves in two dimensions and surfaces in three dimensions. The numerical results give evidence that they are convectively stable. A class of high order three-phase boundary motion problems are also studied. We consider a region where three phase boundaries meet at a triple junction and evolve with specified normal velocities. A system of partial differential algebraic equations (PDAE) is proposed to describe this class of problems by extending the discussion for the coupled surface and grain boundary motion. The linear well-posedness of the system is analyzed and numerical simulations are performed.

Characterisation of the interaction between the neutral atmosphere in Low Earth Orbit and spacecraft surfaces is required for a broad range of applications to system and mission definition. For the prediction of spacecraft trajectories in this Free Molecular regime, the nature of the interaction must be accurately modelled. Accurate definition of the interaction is also required for the design of the attitude control system for vehicles such as Space Station which will generate large aerodynamic moments. The methods available to determine this interaction indirectly from observation of the motion of a satellite are reviewed. The orbital analysis technique is chosen for this study. Two methods of modelling complex spacecraft configurations are developed. The first, a Monte Carlo Test Particle approach, is able to account for all the phenomena characteristic of Free Molecular Flow. The second, adopting a panel method approach, accounts only for the possible shielding of surfaces from the flow. Discrepancies between the two modelling programs are identified but for the limited flow range relevant to the ANS-1 mission, good agreement is found and the computationally more efficient panel method program adopted. A new set of momentum accommodation coefficients are introduced to characterise the interaction. These are resolved in an aerodynamic frame. The new coefficients are found to be more robust than classical surface-resolved models and to have greater sensitivity to the nature of the interaction. The theory required to represent the relationship between the changes in the spacecraft trajectory and the gas-surface interaction is then developed. The sensitivity of the derived momentum accommodation to the parameters used in the modelling process is then determined. The most sensitive parameters are found to be the accuracy of the orbital elements semi-major axis and inclination, the rotation rate of the atmosphere, the temperature of the spacecraft surface and the complexity of the spacecraft configuration model. This theory is then applied to the orbital data derived for ANS-1 (1970-70A) by ESOC. The results suggest that the nature of the interaction is close to the classical diffuse case but the accuracy of the results are limited by uncertainties in the measured changes in orbital inclination.

Raw material accounts for a large proportion (approximately 75 percent) of a sawmill’s operating costs. However, about 15 percent of raw material ends up as low valued sawdust and planer shavings due to inaccurate cutting. Sizable financial benefits can be realized through maximizing conversion of raw material into valuable solid wood. Advanced process control in a sawmill can help achieve straighter cuts closer to final product dimensions and reduce loss of valuable raw material. A novel and practical method for enhanced process control in a sawmill is presented. A laser arrangement consisting of industrial point and line scanners is used to obtain a surface profile of the entire (two-dimensional) top and bottom surfaces of a lumber board. Each surface profile is independent of the other and free of data contamination caused by relative motions between the measured surface and sensors. Point scanners and line scanners simultaneously record 1-D and 2-D height data, respectively, along the length of the board. One-dimensional height data are used to identify relative motions through a mathematical technique based on linear inverse theory. Subtracting relative motion information from raw line scanner data provides an accurate 2-D surface profile. A second line scanner placed below the board can be used to obtain a separate 2-D profile of the bottom lumber surface. Separate-sided profiling is advantageous because typically a different saw or machine mills each side of a board. Thus, knowing the surface profile of each side of a board is crucial not only in diagnosing a deficiency in the milling process but also in determining the location of this deficiency. Results demonstrate that two-dimensional surface profiling can identify common surface defects such as step, washboard and knot tear-out with an accuracy of 0.3mm. Reproduction of each surface is rapid (approximately 0.2 seconds) and stable.

Thesis (Ph. D.) -- University of Maryland, College Park, 2004.
Thesis research directed by: Mathematics. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

In this thesis we address the problem of digitizing the motion of three-dimensional shapes that move and deform in time. These shapes are observed from several points of view with cameras that record the scene's evolution as videos. Using available reconstruction methods, these videos can be converted into a sequence of three-dimensional snapshots that capture the appearance and shape of the objects in the scene. The focus of this thesis is to complement appearance and shape with information on the motion and deformation of objects. In other words, we want to measure the trajectory of every point on the observed surfaces. This is a challenging problem because the captured videos are only sequences of images, and the reconstructed shapes are built independently from each other. While the human brain excels at recreating the illusion of motion from these snapshots, using them to automatically measure motion is still largely an open problem. The majority of prior works on the subject has focused on tracking the performance of one human actor, and used the strong prior knowledge on the articulated nature of human motion to handle the ambiguity and noise inherent to visual data. In contrast, the presented developments consist of generic methods that allow to digitize scenes involving several humans and deformable objects of arbitrary nature. To perform surface tracking as generically as possible, we formulate the problem as the geometric registration of surfaces and deform a reference mesh to fit a sequence of independently reconstructed meshes. We introduce a set of algorithms and numerical tools that integrate into a pipeline whose output is an animated mesh. Our first contribution consists of a generic mesh deformation model and numerical optimization framework that divides the tracked surface into a collection of patches, organizes these patches in a deformation graph and emulates elastic behavior with respect to the reference pose. As a second contribution, we present a probabilistic formulation of deformable surface registration that embeds the inference in an Expectation-Maximization framework that explicitly accounts for the noise and in the acquisition. As a third contribution, we look at how prior knowledge can be used when tracking articulated objects, and compare different deformation model with skeletal-based tracking. The studies reported by this thesis are supported by extensive experiments on various 4D datasets. They show that in spite of weaker assumption on the nature of the tracked objects, the presented ideas allow to process complex scenes involving several arbitrary objects, while robustly handling missing data and relatively large reconstruction artifacts.

Accurate motion capture of deformable objects from monocular video sequences is a challenging Computer Vision problem with immense applicability to domains ranging from virtual reality, animation to image guided surgery. Existing dense motion capture methods rely on expensive setups with multiple calibrated cameras,structured light, active markers or prior scene knowledge learned from a large 3D dataset. In this thesis, we propose an end-to-end pipeline for 3D reconstruction of deformable scenes from a monocular video sequence. Our method relies on a two step pipeline in which temporally consistent video registration is followed by a dense non-rigid structure from motion approach. We present a data-driven method to reconstruct non-rigid smooth surfaces densely, using only a single video as input, without the need for any prior models or shape templates. We focus on the well explored low-rank prior for deformable shape reconstruction and propose its convex relaxation to introduce the first variational energy minimisation approach to non-rigid structure from motion. To achieve realistic dense reconstruction of sparsely textured surfaces, we incorporate an edge preserving spatial smoothness prior into the low-rank factorisation framework and design a single variational energy to address the non-rigid structure from motion problem. We also discuss the importance of long-term 2D trajectories for several vision problems and explain how subspace constraints can be used to exploit the redundancy present in the motion of real scenes for dense video registration. To that end, we adopt a variational optimisation approach to design a robust multi-frame video registration algorithm that combines a robust subspace prior with a total variation spatial regulariser. Throughout this thesis, we advocate the use of GPU-portable and scalable energy minimisation algorithms to progress towards practical dense non-rigid 3D motion capture from a single video in the presence of occlusions and illumination changes.

This PhD thesis collects different experimental studies in the field of wetting phenomena and open microfluidics, which analyze the behavior of liquid drops on free open surfaces. The main goal of such a research is to develop smart coatings featuring useful wetting properties (e. g. water repellent, antifogging and antireflection materials) or techniques aimed at manipulating droplets for chemical or biological applications. In particular this work considers both passive and active methods to control the statics and dynamics of drops deposited on an inclined plane and consequently subject to an external constant force, the gravity force. Among the passive techniques based on surface patterning, we investigated the adhesion properties of multiscale nano- and microstructured hairy surfaces made of polymers having different elasticity. Also, chemically patterned surfaces, formed by hydrophilic and hydrophobic regions of different shape (stripes, squares and triangles), have found to be an effective tool to passively tune drop sliding velocity. Chemically heterogeneous surfaces can affect not only sliding velocity, but also drop trajectory. To further investigate the deviation of a drop by means of a chemical pattern we considered a sample formed by only two regions featuring different wettability, i. e. a chemical step characterized by a linear interface. On the other hand, an active manipulation implies the application of an external field, as, for instance, electric, magnetic or acoustic. As active technique we considered asymmetric vibrations of the substrate, able to induce interesting and surprising dynamical behaviors: small droplets placed on a vertically oscillating inclined plane can stay pinned, slide down, but even climb up the surface against gravity. Even if the vast majority of our experiments involves ordinary liquids, in particular water and aqueous solutions, our research about sliding includes also the study of complex fluids, more precisely polymer solutions, exhibiting rheological properties (e. g. viscosity and elastic behaviors) depending on the applied stress.
Questa tesi raccoglie una serie di lavori sperimentali che si collocano nell'ambito della microfluidica aperta e dei fenomeni interfacciali di bagnamento e fondamentalmente studiano il comportamento di gocce depositate su superfici. Lo scopo principale di questo tipo di ricerca è lo sviluppo di superfici che presentino proprietà particolari, come ad esempio superfici autopulenti, antinebbia o antiriflesso, o di tecniche di manipolazione di gocce finalizzate ad applicazioni nel campo biologico o chimico. In particolare questo lavoro considera metodi attivi e passivi atti a controllare sia la statica che la dinamica di gocce poste su superfici inclinate e quindi soggette ad una forza esterna costante, la forza di gravità. Tra le tecniche passive basate sull'utilizzo di superfici strutturate sono state studiate le proprietà di adesione di superfici polimeriche geometricamente nano/microstrutturate. Inoltre, campioni chimicamente eterogenei formati da regioni idrofiliche e idrofobiche di geometria diversa (strisce, quadrati, triangoli) si sono dimostrati uno strumento efficace per la regolazione passiva della velocità di scivolamento delle gocce. Questo tipo di superfici può influire non solo sulla velocità, ma anche sulla traiettoria della goccia. Per analizzare più nel dettaglio come si può deviare una goccia è stato studiato lo scivolamento su una superficie formata da due sole regioni di diversa bagnabilità, cioè una sorta di gradino chimico. D'altra parte, un controllo attivo implica l'applicazione di un campo esterno, ad esempio elettrico, magnetico o acustico. Come tecnica attiva in questa tesi è stata considerata l'applicazione di vibrazioni asimmetriche del substrato, capaci di indurre comportamenti dinamici interessanti e sorprendenti: piccole goccioline poste su un piano inclinato che oscilla verticalmente possono non solo rimanere ferme o scivolare, ma addirittura risalire contro la forza di gravità. Anche se la maggioranza di questi esperimenti riguarda liquidi ordinari, in particolare acqua e soluzioni acquose, una parte della ricerca è stata dedicata allo scivolamento di fluidi complessi, più precisamente soluzioni polimeriche, caratterizzati da proprietà reologiche (ad esempio viscosità o effetti elastici) che dipendono dallo sforzo applicato sul fluido.

Due to the wide field of view, omnidirectional cameras have been extensively used in many applications, including surveillance and autonomous navigation. In order to implement a fully autonomous system, one of the essential problems is construction of an accurate, dynamic environment model. In Computer Vision this is called structure from stereo or motion (SFSM). The work in this dissertation addresses omnidirectional vision based SFSM for the navigation of an autonomous surface vehicle (ASV), and implements a vision system capable of locating stationary obstacles and detecting moving objects in real time. The environments where the ASV navigates are complex and fully of noise, system performance hence is a primary concern. In this dissertation, we thoroughly investigate the performance of range estimation for our omnidirectional vision system, regarding to different omnidirectional stereo configurations and considering kinds of noise, for instance, disturbances in calibration, stereo configuration, and image processing. The result of performance analysis is very important for our applications, which not only impacts the ASVâ s navigation, also guides the development of our omnidirectional stereo vision system. Another big challenge is to deal with noisy image data attained from riverine environments. In our vision system, a four-step image processing procedure is designed: feature detection, feature tracking, motion detection, and outlier rejection. The choice of point-wise features and outlier rejection based method makes motion detection and stationary obstacle detection efficient. Long run outdoor experiments are conducted in real time and show the effectiveness of the system.
Ph. D.

In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as Electrostatic Potential (EP) and hydropathy expressed as Molecular Lipophilic Potential (MLP). The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by phisicochemical programs and visualized as range of colours that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of colour to encode both characteristics makes the simultaneous visualization almost impossible. This is why most of the times EP and MLP are presented in two different images. In this thesis, we describe a novel and intuitive code for the simultaneous visualization of these properties. For our purpose we use Blender, an open-source, free, cross-platform 3D application used for modelling, animation, gaming and rendering. On the basis of Blender, we developed BioBlender, a package dedicated to biological work: elaboration of proteins motion with the simultaneous visualization of their chemical and physical features. Blender's Game Engine, equipped with specific physico-chemical rules is used to elaborate the motion of proteins, interpolating between different conformations (NMR collections or different X-rays of the same protein). We obtain a physically plausible sequence of intermediate conformations which are the basis for the subsequent visual elaboration. A new visual code is introduced for MLP visualization: a range of optical features that goes from dull-rough surfaces for the most hydrophilic areas to shiny-smooth surfaces for the most lipophilic ones. This kind of representation permits a photorealistic rendering of the smooth spatial distribution of the values of MLP on the surface of the protein. EP is represented as animated line particles that flow along field lines, from positive to negative, proportional to the total charge of the protein. Our system permits EP and MLP simultaneous visualization of molecules and, in the case of moving proteins, the continuous perception of these features, calculated for each intermediate conformation. Moreover, this representation contributes to gain insight into the molecules function by drawing viewer's attention to the most active regions of the protein.